Eden McCain -- Eden tries to use her power of persuasion to convince Sylar to commit suicide with a gun that she will give him, but he manages to stop her. When he threatens to steal her power, she shoots herself in the head, thereby preventing him from doing so. (Fallout)

Claire Bennet -- Sylar removes the top of her skull, and examines her brain while she is still conscious. She asks if he will eat her brain, to which he replies: "that's disgusting." After gaining her power, he says she can't die, and replaces her skull, which then heals. (The Butterfly Effect)

Claire was unable to regenerate until the branch was pulled from her brain. (One Giant Leap, Collision) Peter was similarly unable to regenerate until the shard of glass was removed from his brain. (.07%)

In The Second Coming, Sylar acquires Claire's power without (permanently) removing her brain at all. This could indicate that he only removes the other victims' brains due to a combination of either lack of time to study them at the scene and/or because their survival (unlike Claire's) is already impossible. In any case, he indicates disgust at the idea of ingesting someone's brain when asked by Claire.

Saving Charlie refers to Sylar's process of removing the top few inches of his victims' heads as "hemicapitation" (Chapter 34). The book also notes that a painting of Saint Nicasius shows that the top of his head had been removed, "his soul sparkling up to heaven" (Chapter 42). When Hiro researches this, he finds that this was done to "let out the evil spirits". He also reads about the process of "trepanning", an actual process of opening the skull, usually by boring holes in it. Hiro finds that the "primitive form of brain surgery" is performed as far back as 10,000 BC in Egypt, Rome, India, Africa, and Central America. He also learns that the Zapotecs and other Native American tribes would grind up skulls and make medicines from the bones, "as a way of stealing their enemies' power". Hiro then teleports to an ancient setting and witnesses a Zapotec shaman about to perform a trepanning ritual (Chapter 43).